Package ffx.algorithms.cli

Class AnnealOptions

java.lang.Object
ffx.algorithms.cli.AnnealOptions
public class AnnealOptions extends Object
Represents command line options for scripts that utilize simulated annealing.
Since:
1.0
Author:
Michael J. Schnieders, Jacob M. Litman

  • Constructor Details

    • AnnealOptions

      public AnnealOptions()

  • Method Details

    • getWindows

      public int getWindows()
      Number of annealing windows.
      Returns:
      Returns the number of windows.

    • createAnnealer

      public SimulatedAnnealing createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)
      Creates a SimulatedAnnealing object.
      Parameters:
      dynamicsOptions - Dynamics options to use.
      molecularAssembly - MolecularAssembly
      potential - Potential
      algorithmListener - AlgorithmListener
      Returns:
      SimulatedAnnealing

    • createAnnealer

      public SimulatedAnnealing createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile)
      Creates a SimulatedAnnealing object.
      Parameters:
      dynamicsOptions - Dynamics options to use.
      molecularAssembly - MolecularAssembly
      potential - Potential
      algorithmListener - AlgorithmListener
      dynFile - Dynamics restart file.
      Returns:
      SimulatedAnnealing

    • getSchedule

      public AnnealingSchedule getSchedule()
      Constructs an AnnealingSchedule.
      Returns:
      An AnnealingSchedule.

    • setWindows

      public void setWindows(int windows)

    • getLow

      public double getLow()
      Low temperature limit in degrees Kelvin.
      Returns:
      Returns the low temperature limit.

    • setLow

      public void setLow(double low)

    • getUpper

      public double getUpper()
      Upper temperature limit in degrees Kelvin.
      Returns:
      Returns the upper temperature limit.

    • setUpper

      public void setUpper(double upper)

    • isReinitVelocities

      public boolean isReinitVelocities()
      Forces simulated annealing to re-initialize velocities to the new temperature at each annealing step, rather than letting the thermostat shift temperature downwards.
      Returns:
      Returns true for re-initialization of velocities.

    • setReinitVelocities

      public void setReinitVelocities(boolean reinitVelocities)

    • getTemperString

      public String getTemperString()
      Sets the schedule to be used.
      Returns:
      Returns a String representation of the tempering schedule.

    • setTemperString

      public void setTemperString(String temperString)

    • getTemperBefore

      public int getTemperBefore()
      Sets the number of annealing windows to hold flat at the high temperature (in addition to normal windows).
      Returns:
      Returns the number of annealing windows to hold flat at the high temperature.

    • setTemperBefore

      public void setTemperBefore(int temperBefore)

    • getTemperAfter

      public int getTemperAfter()
      Sets the number of annealing windows to hold flat at the low temperature (in addition to normal windows).
      Returns:
      Returns the number of annealing windows to hold flat at the low temperature.

    • setTemperAfter

      public void setTemperAfter(int temperAfter)